Hi,
See below...
> Hi I would like to use a ventral striatal mask from the striatum-con-prob-thr50 atlas. I see that there are several options in the atlas directory:
>
> striatum-con-label-thr50-7sub-1mm.nii.gz
> striatum-con-prob-thr50-1mm.nii.gz
> striatum-structural-1mm.nii.gz
>
> Here are my questions:
> 1. Are these in MNI space? I overlaid them on the MNI 1 mm standard and they seem to overlap fairly well.
Yes - it is in MNI space.
> 2. Which one of these should I use if I want a ventral striatum seed mask for probtrackx?
The striatum-con-label-thr50-7sub-1mm.nii.gz one is probably the best one, as it takes into account the overlap of neighbouring regions and is already thresholded.
> 3. Should I first transform the striatum structural 1 mm seed mask to my T1 subject image and then run probtrackx?
> 4. Or should I transform my T1 and Diffusion nodif mask to MNI space and then use the seed mask as is to run tractography?
> 5. Should I use FNIRT or FLIRT for any registration and what settings?
With FDT (which is especially easy through the GUI) you can specify your mask in whatever space you want, together with the transformations between spaces. Sounds like you only need the transformation between the T1 and the MNI space and for that you should use FNIRT (which requires an initial 12 DOF FLIRT for initialisation). You can find instructions on how to do this on the wiki or in the registration practical of the FSL Course.
All the best,
Mark
>
> (My T1 and Diffusion are already in the same space.)
>
> -AB
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